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Forensic STR and SNP Genotyping of Formalin-Fixed Skeleton Samples With Illumina's ForenSeq System
Tingting Yang1,2, Linlin Gao3, Jiarong Zhang1,2
1School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China.
Electrophoresis
|October 15, 2024
Summary
Formalin fixation degrades DNA in skeletal samples over time, impacting forensic genetic analysis. Massively parallel sequencing (MPS) shows promise for analyzing degraded DNA, but detection rates decrease with longer fixation periods.
Area of Science:
- Forensic Science
- Genetics
- Molecular Biology
Background:
- Formalin fixation is standard for preserving forensic tissues, but DNA extraction and typing, especially short tandem repeat (STR) analysis, are challenging.
- Massively parallel sequencing (MPS) offers a high-throughput method for analyzing numerous genetic markers, including single-nucleotide polymorphisms (SNPs) and STRs, making it suitable for degraded evidence.
Purpose of the Study:
- To evaluate the effectiveness of massively parallel sequencing (MPS) for genotyping short tandem repeats (STRs) and single-nucleotide polymorphisms (SNPs) in formalin-fixed skeletal samples.
- To determine the impact of formalin fixation duration on DNA quality and the detection rates of forensic genetic markers.
Main Methods:
- Skeletal samples from 5 individuals, fixed for 5-75 days, were analyzed using the ForenSeq DNA Signature Prep Kit on the Illumina MiSeq FGX platform.
- Detection rates and cumulative discrimination power (CDP) for STRs and SNPs were assessed in relation to formalin fixation time.
Main Results:
- Detection rates for both STRs and SNPs decreased significantly with increased formalin fixation duration.
- After 75 days of fixation, average detection rates for STRs and SNPs were only 4% and 10%, respectively.
- While SNP genotyping maintained a high cumulative discrimination power (>0.9999) up to 45 days, STR genotyping's CDP dropped to 0.9930 by day 22.
Conclusions:
- DNA extracted from formalin-fixed skeletons degrades rapidly, with longer fixation times severely reducing marker detection.
- Massively parallel sequencing (MPS) is a viable tool for forensic genetic analysis of degraded formalin-fixed samples, but its efficiency is time-dependent.
- Specific STRs and SNPs showed consistently low detection rates, suggesting potential limitations for certain markers in degraded samples.
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